Enzymes II

Question 1

what is a perfect enzyme?

Answer 1

enzyme that catalyses a reaction so efficiently that the rate-limiting step is that of substrate diffusion into the active site.

Question 2

what is an example of a ‘perfect’ enzyme?

Answer 2

• triosephosphate isomerase (TIM).
• catalyses the conversion of Dihydroxyacetone Phosphate & Glyceraldehyde 3-Phosphate (the two 3C intermediates in glycolysis)

Question 3

how do perfect enzymes work?

Answer 3

• instead of there being a big energy change and the reaction happening by conversion of A to Z
• it happens via intermediates that don’t have a high energy change between them, making the conversion easier.
• the reaction is limited by E + S (substrate diffusion into the enzyme), so decreasing the energy levels doesn’t increase the efficiency/rate of reaction.

Question 4

how do serine proteases work and give an example

Answer 4

• they attack peptide bond to form acyl-enzyme which is easily hydrolysed
• have a sequence specificity so that they do not cleave all peptide bonds

eg: chymotrypsin made in the pancreas

Question 5

what is the catalytic triad?

Answer 5

• Ser 195 may get its reactivity due to its positioning next to His 57 and Asp 102.
• this is a catalytic triad, which makes the serine much more electronegative.
• triad is found in all proteases.

Question 6

how does trypsin work?

Answer 6

cleaves after Lys, Arg (which are positively charged), due to its negative pocket/cleft

Question 7

how does chymotrypsin work?

Answer 7

cleaves after Phe, Trp, Tyr (which are aromatic and hydrophobic) due to its hydrophobic pocket/cleft

Question 8

hoe does elastase work?

Answer 8

cleaves after small amino acids (with a small R group) due to its narrow pocket/cleft.

Question 9

how does ATP synthase work?

Answer 9

• ATP Catalysis begins when protons pass through the part of the enzyme that lies in the cell membrane, causing it to turn.
• the central core then rotates inside the top half of the enzyme.
• this region holds an ATP molecule and pulls in ADP and an inorganic phosphate group in the neighbouring subunit.
• as the core rotates, the subunit with ATP loosens, and the section holding ADP closes.
• the original ATP molecule is released, and a new one is formed from the ADP.
• the cycle repeats.

Question 10

highlight how topoisomerase II works

Answer 10

• the G-segment (gate segment) of the chromosome binds to the Topoisomerase II.
• ATP is used to clamp the T-segment (target segment) of the chromosome.
• the G-segment is broken, and the T-segment is pulled through.
• the G-segment is resealed and released via ATP hydrolysis.